Resurgence of Bordetella pertussis, including one macrolide-resistant isolate, France, 2024

As other European countries, France is experiencing a resurgence of pertussis in 2024. Between 1 January and 31 May 2024, 5,616 (24.9%) positive Bordetella pertussis qPCR tests were identified, following a 3-year period of almost null incidence. Of 67 cultured and whole genome sequenced B. pertussis isolates, 66 produced pertactin and 56 produced FIM2, in contrast to pre-COVID-19 years. One isolate of genotype Bp-AgST4 was resistant to macrolides. Pertussis resurgence may favour isolates that produce FIM2 and pertactin.


Supplementary text 1: Statistical Analyses
We conducted a quasi-experimental interrupted time series analysis relying on negative binomial regression models, with a time unit of 1 month, to analyze the changes in the incidence of positive Bordetella PCRs over time.All positive PCR results were included in the models.The models accounted for seasonality (using one pair of sine/cosine terms), a binary variable to define periods before and after the COVID-19 pandemic (this variable was coded 0 before April 2020, 1 between April 2020 and December 2023, and 2 starting in January 2024) and overdispersion of data.The models also included a dummy variable (with 36-month periods) to adjust for long-term cycles commonly observed in pertussis epidemiology.In such models, an incidence rate ratio (IRR) greater than 1 indicates that the corresponding variable is associated with an increase in pertussis incidence.We also conducted a sensitivity analysis in which seasonality was adjusted using calendar month.We used Stata/SE 18.0 (StataCorp LP, College Station, TX, United States) for all analyses.Based on this dataset, four different genotypes of MRBP isolates were identified:

Supplementary text 2: genomic analysis of international macrolide-resistant B. pertussis
-ptxP1-MRBP1 clade grouped macrolide resistant isolates originating mostly from China, with 2 genomes from Japan (3) and 2 from the USA.All were characterized by a Bp-AgST37 (characterized by a ptxP1 and fhaB3 genotype), as defined in Bridel et al. 2022 (1).
-one ptxP1-MRBP2 clade contained only one macrolide-resistant isolate A228 collected in 1994 in the USA (4) in Arizona.This isolate was Bp-AgST8, characterized by ptxP1 and fhaB1 alleles.
-the clade ptxP3-MRBP1 contained the macrolide resistant isolate ATCC BAA1335 collected in 1999 in the USA (5), with genotype Bp-AgST4, characterized by a ptxP3 and fhaB1 alleles.
-the clade ptxP3-MRBP2 contained 5 macrolide resistant isolates: 1 from France collected in 2024 (FR7302) and 4 from China (P745 and Bp20, BP0066 and GZBP22005).All were Bp-AgST4, with ptxP3, fhaB1 and fim3-1 alleles.The MRBP isolate collected in France in 2024 (FR7302) was found to be phylogenetically associated with ptxP3-MRBP3 P745 isolate from Shanghai (2022) characterized by a MT28 MLVA profile (2).Only 2 cgMLST loci differed between these two isolates.These two isolates were also closely related to 2 other macrolide resistant isolates, BP0066 and GZBP22005, both collected in China but also to another MT28 isolate from China (P20), susceptible to macrolides ( 2 phylogenetic analysis was performed focusing on B. pertussis isolates resistant to macrolides (MRBP), based on the dataset described in Bridel et al. 2022 (1), supplemented with genomes from Wu et al. (2) downloaded from NCBI, and adding all French isolates from 2024 (n=186).